Enzyme-Substrate Binding

Enzyme–Substrate Binding

In an enzyme-catalyzed reaction, the enzyme binds to the substrate (one of the reactants) to form a complex. The formation of the complex leads to the formation of the transition-state species, which then forms the product. The nature of transition states in enzymatic reactions is a large Þeld of research in itself, but some general statements can be made on the subject. A substrate binds, usually by noncovalent interactions, to a small portion of the enzyme called the active site, frequently situated in a cleft or crevice in the protein and consistingof certain amino acids that are essential for enzymatic activity (Figure 6.3). The catalyzed reaction takes place at the active site, usually in several steps.

Why do enzymes bind to substrates?

The Þrst step is the binding of substrate to the enzyme, which occurs because of highly speciÞc interactions between the substrate and the side chains and backbone groups of the amino acids making up the active site. Two important models have been developed to describe the binding process. The Þrst, the lock-and-key model, assumes a high degree of similarity between the shape of the substrate and the geometry of the binding site on the enzyme (Figure 6.3a). The substrate binds to a site whose shape complements its own, like a key in a lock or the correct piece in a three-dimensional jigsaw puzzle. This model has intuitive appeal but is now largely of historical interest because it does not take into account an important property of proteins, namely their conformational ßexibility. 

The second model takes into account the fact that proteins have some three-dimensional ßexibility. According to this induced-fit model, the binding of the substrate induces a conformational change in the enzyme that results in a complementary Þt after the substrate is bound (Figure 6.3b). The binding site has a different three-dimensional shape before the substrate is bound. The induced-Þt model is also more attractive when we consider the nature of the transition state and the lowered activation energy that occurs with an enzyme-catalyzed reaction. The enzyme and substrate must bind to form the ES complex before anything else can happen. What would happen if this binding were too perfect? Figure 6.4 shows what happens when E and S bind. An attraction must exist between E and S for them to bind. This attraction causes the ES complex to be lower on an energy diagram than the E + S at the start. Then the bound ES must attain the conformation of the transition state EX^à. If the binding of E and S to form ES were a perfect Þt, the ES would be at such a low energy that the difference between ES and EX^à would be very large. This would slow down the rate of reaction. Many studies have shown that enzymes increase the rate of reaction by lowering the energy of the transition state, EX^à, while raising the energy of the ES complex. The induced-Þt model certainly supports this last consideration better than the lock-and-key model; in fact, the induced-Þt model mimics the transition state.

After the substrate is bound and the transition state is subsequently formed, catalysis can occur. This means that bonds must be rearranged. In the tran-sition state, the substrate is bound close to atoms with which it is to react. Furthermore, the substrate is placed in the correct orientation with respect to those atoms. Both effects, proximity and orientation, speed up the reaction. As bonds are broken and new bonds are formed, the substrate is transformed into product. The product is released from the enzyme, which can then catalyze the reaction of more substrate to form more product (Figure 6.5). 

Each enzyme has its own unique mode of catalysis, which is not surprising in view of enzymesÕ great specificity. Even so, some general modes of catalysis exist in enzymatic reactions. Two enzymes, chymotrypsin and aspartate transcarbamoylase, are good examples of these general principles.

Summary

Before a reaction can be catalyzed, the enzyme and substrate must bind.The substrate binds to the enzyme in a special pocket called the active site.

Binding to the active site is reversible and occurs through noncovalent interactions.

Two models are often used to describe the binding: the lock-and-key model and the induced-fit model.

The induced-fit model is the more accurate description of formation of the ES complex, as it explains how the binding of E + S leads toward establishment of the transition state.